Abstract The Human BioMolecular Atlas Program (HuBMAP) will redefine our understanding of the human body by recovering multi-scale tissue organization -- anatomical, histological, and molecular, at unprecedented resolution, through computational integration of diverse experimental measurements. We propose to develop computational methods and tools to enable the use of HuBMAP collected data by consortium participants, the international research community and the large software and method development community. Our proposal is focused on three key directions for the Tools Component: (1) Community involvement: Development of repositories, APIs, interfaces and schemas to enable the hosting, discovery and integration of tools and libraries developed by us and others. We would put specific emphasis on making sure that this process is efficient, reduces duplicated efforts and transparent enabling involvement of the general developer community. All tools would be developed as open source software. (2) Innovative tool development: While we intend to rely and use existing tools as much as possible, we also propose to develop a comprehensive set of innovative tools for the specific challenges presented by the HuBMAP long term vision and data. These include tools for querying and retrieving data collected by the HUBMAP, expression and image analysis methods and libraries, tools for the analysis of spatial and temporal data from the MAP and tools for modeling and data integration which would enable the integration of HuBMAP data with the vast amounts of other publicly available biological data. (3) Flexibility: We expect that improved technology and variance in the specific plans of the Tissue Mapping Centers would lead to additional types of data that we have not designed tools for in the past. We have thus assembled an experienced and diverse group of investigators, all with significant experience in tool development that, together, span the spectrum of potential types of data. Our proposal includes detailed plans for ensuring that the tools we develop and implement are findable, accessible, interoperable and reusable (FAIR) and addresses issues related to validation of tool accuracy and usefulness, data privacy and reproducibly. The Tools component would work very closely with other HIVE components to disseminate the tools and to connect with both the developers and the international research communities.